I'm sorry, but an important part of this interview is objectively wrong.
Ninjas are not real people, the whole concept was based largely on shinobi (and also in part Kabuki theater stagehands, long story), who were mostly spies and saboteurs. I'm not saying they were not capable of assassinations or that they hadn't carried them out, but they were not some shadowy order of elite warrior assassins, just a bunch of mostly down-on-their-luck folks, who found a way to get by in the shadows of their society. Society, which, I dare add, has in that particular time period closed itself to most of the outside world and its military technology with it and which has at the time suffered from a major shortage of quality iron further contributing to high prices and low availability of usable combat equipment, especially outside of the highly privileged warrior caste.
Pirates on the other hand have in that particular time period had access to reasonably well armed ships (guns, cannons, you name it) and given the fact they were sailors, they've spent long stretches of time in large groups, something shinobi would have a hard time with while on assignments given the fact they had to keep a low profile. If you portray the "ninja" as a specialized assassin, the pirate might as well be a skeleton made undead by swiping cursed Aztec gold.
Not only do pirates win hands down in this particular case, it should also be considered that while ninjutsu is (to our knowledge, limited as it may be, I grudgingly admit) only trained as something martial art-ish without focus on direct real world applications, real world pirates are still out and about and as ever, they have access to dangerous ship-based weapons (though luckily not anything as significant as a frigate in XVIIIth century) such as cannons and torpedoes, you can also expect them to be armed with modern firearms, which means if we're discussing absolute apex examples of pirate vs ninja/shinobi, the pirate is a XXIst century Somalian with an AK47 and a bad temper.
This is srs bsns!